chr19-50377484-T-C
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000597157.1(NR1H2):c.-122T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.625 in 885,204 control chromosomes in the GnomAD database, including 178,741 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.70 ( 38493 hom., cov: 28)
Exomes 𝑓: 0.61 ( 140248 hom. )
Consequence
NR1H2
ENST00000597157.1 5_prime_UTR
ENST00000597157.1 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.301
Genes affected
NR1H2 (HGNC:7965): (nuclear receptor subfamily 1 group H member 2) The liver X receptors, LXRA (NR1H3; MIM 602423) and LXRB, form a subfamily of the nuclear receptor superfamily and are key regulators of macrophage function, controlling transcriptional programs involved in lipid homeostasis and inflammation. The inducible LXRA is highly expressed in liver, adrenal gland, intestine, adipose tissue, macrophages, lung, and kidney, whereas LXRB is ubiquitously expressed. Ligand-activated LXRs form obligate heterodimers with retinoid X receptors (RXRs; see MIM 180245) and regulate expression of target genes containing LXR response elements (summary by Korf et al., 2009 [PubMed 19436111]).[supplied by OMIM, Jan 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NR1H2 | NM_007121.7 | c.-19-103T>C | intron_variant | ENST00000253727.10 | |||
NR1H2 | NM_001256647.3 | c.-19-103T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NR1H2 | ENST00000253727.10 | c.-19-103T>C | intron_variant | 1 | NM_007121.7 | P1 |
Frequencies
GnomAD3 genomes AF: 0.695 AC: 105198AN: 151412Hom.: 38414 Cov.: 28
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GnomAD4 exome AF: 0.611 AC: 448040AN: 733674Hom.: 140248 Cov.: 10 AF XY: 0.613 AC XY: 232632AN XY: 379370
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GnomAD4 genome AF: 0.695 AC: 105341AN: 151530Hom.: 38493 Cov.: 28 AF XY: 0.696 AC XY: 51486AN XY: 74016
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at